Persistent Homology Over Directed Acyclic Graphs

We define persistent homology groups over any set of spaces which have inclusions defined so that the corresponding directed graph between the spaces is acyclic, as well as along any subgraph of this directed graph. This method simultaneously generalizes standard persistent homology, zigzag persistence and multidimensional persistence to arbitrary directed acyclic graphs, and it also allows the study of more general families of topological spaces or point-cloud data. We give an algorithm to compute the persistent homology groups simultaneously for all subgraphs which contain a single source and a single sink in $O(n^4)$ arithmetic operations, where $n$ is the number of vertices in the graph. We then demonstrate as an application of these tools a method to overlay two distinct filtrations of the same underlying space, which allows us to detect the most significant barcodes using considerably fewer points than standard persistence.Comment: Revised versio

Vaccines against toxoplasma gondii : challenges and opportunities

Development of vaccines against Toxoplasma gondii infection in humans is of high priority, given the high burden of disease in some areas of the world like South America, and the lack of effective drugs with few adverse effects. Rodent models have been used in research on vaccines against T. gondii over the past decades. However, regardless of the vaccine construct, the vaccines have not been able to induce protective immunity when the organism is challenged with T. gondii, either directly or via a vector. Only a few live, attenuated T. gondii strains used for immunization have been able to confer protective immunity, which is measured by a lack of tissue cysts after challenge. Furthermore, challenge with low virulence strains, especially strains with genotype II, will probably be insufficient to provide protection against the more virulent T. gondii strains, such as those with genotypes I or II, or those genotypes from South America not belonging to genotype I, II or III. Future studies should use animal models besides rodents, and challenges should be performed with at least one genotype II T. gondii and one of the more virulent genotypes. Endpoints like maternal-foetal transmission and prevention of eye disease are important in addition to the traditional endpoint of survival or reduction in numbers of brain cysts after challenge

A re-evaluation of the magnitude and impacts of anthropogenic atmospheric nitrogen inputs on the ocean

We report a new synthesis of best estimates of the inputs of fixed nitrogen to the world ocean via atmospheric deposition, and compare this to fluvial inputs and di-nitrogen fixation. We evaluate the scale of human perturbation of these fluxes. Fluvial inputs dominate inputs to the continental shelf, and we estimate about 75% of this fluvial nitrogen escapes from the shelf to the open ocean. Biological di-nitrogen fixation is the main external source of nitrogen to the open ocean, i.e. beyond the continental shelf. Atmospheric deposition is the primary mechanism by which land based nitrogen inputs, and hence human perturbations of the nitrogen cycle, reach the open ocean. We estimate that anthropogenic inputs are currently leading to an increase in overall ocean carbon sequestration of ~0.4% (equivalent to an uptake of 0.15 Pg C yr-1 and less than the Duce et al., 2008 estimate). The resulting reduction in climate change forcing from this ocean CO2 uptake is offset to a small extent by an increase in ocean N2O emissions. We identify four important feedbacks in the ocean atmosphere nitrogen system that need to be better quantified to improve our understanding of the perturbation of ocean biogeochemistry by atmospheric nitrogen inputs. These feedbacks are recycling of (1) ammonia and (2) organic nitrogen from the ocean to the atmosphere and back, (3) the suppression of nitrogen fixation by increased nitrogen concentrations in surface waters from atmospheric deposition, and (4) increased loss of nitrogen from the ocean by denitrification due to increased productivity stimulated by atmospheric inputs

Signatures of a dissipative phase transition in photon correlation measurements

This work was supported by the Swiss National Science Foundation (SNSF) through the National Centre of Competence in Research - Quantum Science and Technology (NCCR QSIT). A.S., C.S., and S.H. acknowledge support by the State of Bavaria and the DFG within the Project Schn1376/3-1.Understanding and characterizing phase transitions in driven-dissipative systems constitutes a new frontier for many-body physics[1-8]. A generic feature of dissipative phase transitions is a vanishing gap in the Liouvillian spectrum [9], which leads to long-lived deviations from the steady state as the system is driven towards the transition. Here, we show that photon correlation measurements can be used to characterize the corresponding critical slowing down of non-equilibrium dynamics. We focus on the extensively studied phenomenon of optical bistability in GaAs cavity polaritons [10,11], which can be described as a first-order dissipative phase transition [12-14]. Increasing the excitation strength towards the bistable range results in an increasing photon-bunching signal along with a decay time that is prolonged by more than nine orders of magnitude as compared with that of single polaritons. In the limit of strong polariton interactions leading to pronounced quantum fluctuations, the mean-field bistability threshold is washed out. Nevertheless, the functional form with which the Liouvillian gap closes as the thermodynamic limit is approached provides a signature of the emerging dissipative phase transition. Our results establish photon correlation measurements as an invaluable tool for studying dynamical properties of dissipative phase transitions without requiring phase-sensitive interferometric measurements.PostprintPeer reviewe

The processing and impact of dissolved riverine nitrogen in the Arctic Ocean

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Estuaries and Coasts 35 (2012): 401-415, doi:10.1007/s12237-011-9417-3.Although the Arctic Ocean is the most riverine-influenced of all of the world’s oceans, the importance of terrigenous nutrients in this environment is poorly understood. This study couples estimates of circumpolar riverine nutrient fluxes from the PARTNERS (Pan-Arctic River Transport of Nutrients, Organic Matter, and Suspended Sediments) Project with a regionally configured version of the MIT general circulation model to develop estimates of the distribution and availability of dissolved riverine N in the Arctic Ocean, assess its importance for primary production, and compare these estimates to potential bacterial production fueled by riverine C. Because riverine dissolved organic nitrogen is remineralized slowly, riverine N is available for uptake well into the open ocean. Despite this, we estimate that even when recycling is considered, riverine N may support 0.5–1.5 Tmol C year−1 of primary production, a small proportion of total Arctic Ocean photosynthesis. Rapid uptake of dissolved inorganic nitrogen coupled with relatively high rates of dissolved organic nitrogen regeneration in N-limited nearshore regions, however, leads to potential localized rates of riverine-supported photosynthesis that represent a substantial proportion of nearshore production.Funding for this work was provided through NSFOPP- 0229302 and NSF-OPP-0732985.Support to SET was additionally provided by an NSERC Postdoctoral Fellowship

Environmental effects of ozone depletion, UV radiation and interactions with climate change : UNEP Environmental Effects Assessment Panel, update 2017

Peer reviewe

H2S events in the Peruvian oxygen minimum zone facilitate enhanced dissolved Fe concentrations

Dissolved iron (DFe) concentrations in oxygen minimum zones (OMZs) of Eastern Boundary Upwelling Systems are enhanced as a result of high supply rates from anoxic sediments. However, pronounced variations in DFe concentrations in anoxic coastal waters of the Peruvian OMZ indicate that there are factors in addition to dissolved oxygen concentrations (O2) that control Fe cycling. Our study demonstrates that sediment-derived reduced Fe (Fe(II)) forms the main DFe fraction in the anoxic/euxinic water column off Peru, which is responsible for DFe accumulations of up to 200 nmol L-1. Lowest DFe values were observed in anoxic shelf waters in the presence of nitrate and nitrite. This reflects oxidation of sediment-sourced Fe(II) associated with nitrate/nitrite reduction and subsequent removal as particulate Fe(III) oxyhydroxides. Unexpectedly, the highest DFe levels were observed in waters with elevated concentrations of hydrogen sulfide (up to 4 µmol L-1) and correspondingly depleted nitrate/nitrite concentrations (<0.18 µmol L-1). Under these conditions, Fe removal was reduced through stabilization of Fe(II) as aqueous iron sulfide (FeSaqu) which comprises complexes (e.g., FeSH+) and clusters (e.g., Fe2S2|4H2O). Sulfidic events on the Peruvian shelf consequently enhance Fe availability, and may increase in frequency in future due to projected expansion and intensification of OMZs

Bat overpasses: An insufficient solution to restore habitat connectivity across roads

International audienceRoads have many negative effects on wildlife, including their role in habitat fragmentation. Habitat fragmentation affects bats during their daily movements between roosts and foraging areas. As bats are protected in Europe, developers must implement specific mitigation measures that are hierarchically structured to achieve a null net impact. However, very few specific mitigation measures have been undertaken specifically for bats. Bat overpasses (e.g. gantries) are among proposed improvements intended to reduce the impact of roads, but they have rarely been tested. The effectiveness of overpasses in facilitating safe road crossing of bats is critical for justifying the implementation of this mitigation measure. We therefore assessed whether bat overpasses are effectively used by bats. We studied three bat overpasses with different designs in France. We developed an innovative method to characterize bat crossings using acoustic flight path reconstruction (AFPR). We used six pairs of stereo acoustic recorders in different habitat types that were located on both sides of the road, and operated simultaneously throughout the night. Recording data contained 57,941 bat passes and 284 bat crossings from six species of bats at the three study sites. Our results suggest that crossings are more numerous if an overpass is located where bat commuting routes have been identified by environmental impact assessment. However, we found that the proportion of bat crossings along the commuting route was the same with or without an overpass; thus highlighting that bat overpasses do not fully restore habitat connectivity. Synthesis and applications. Our study demonstrates that acoustic flight path reconstruction (AFPR) is a useful approach to obtain information on bat flight behaviour. We also emphasize the importance of field testing the effectiveness of mitigation measures, such as those intended to offset the impact of roads on biodiversity, and highlight that such measures should not be implemented based on their theoretical effectiveness alone